Inspired by & based on Mothur Miseq SOP Please try interactive mode before batch mode (to know what happens within each command)
Please check numeric parameters within batch file before running it. start from here change the name of the file from stability.files to whatever suits your study make.contigs(file=stability.files, processors=4) summary.seqs(fasta=stability.trim.contigs.fasta) screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, summary=stability.trim.contigs.summary, maxambig=0, maxlength=275)
summary.seqs(fasta=stability.trim.contigs.good.fasta) unique.seqs(fasta=stability.trim.contigs.good.fasta) count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)
summary.seqs(count=stability.trim.contigs.good.count_table)
###pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=8) rename.